tbuckley/cabot-search huggingface dataset:
Letter to the Editor: More questions than answers—Response to the POP-NEXT project
Authors: Philip Berry, Sreelakshmi Kotha
Journal: Hepatology (2023)

To the editor, Ratziu et al's1 fascinating survey of clinical variability in the diagnosis and management of NAFLD emphasizes the uncertain place that it occupies in the field of hepatology. Is it a liver condition or one manifestation of a metabolic disorder? Is the hepatogastroenterologist responsible for "managing the liver" or the whole person? Does NAFLD's extremely high prevalence present an insurmountable challenge for public health systems, thus explaining the tendency in some countries for patients to be referred back to primary care? Are continuing attempts to find effective therapies targeted at inflammation and fibrosis just ignoring what appears to be the proximate cause in the majority of cases, obesity?2,3 The authors should be congratulated for avoiding a judgmental tone in the narrative; however, implicit in their paper is the expectation that specialists should conduct a multisystem assessment (sleep apnea, kidney disease, and cardiovascular risk), and extend their responsibilities to prescribing statins when appropriate. In reality, the number of patients presenting to clinics means that such comprehensive assessment is not possible, and it is reasonable to request that primary physicians lead on these aspects. It is interesting to note that decisions and interventions that sit comfortably within the skill sets and influence of specialists (such as hepatoma screening, liver biopsy, and long-term follow-up of mild disease) were done more frequently—perhaps to an inappropriate degree—than interventions likely to be a greater overall benefit in terms of survival, for example, cardiovascular risk assessment.4 This survey of hepatogastroenterologists affords, inevitably, a narrow perspective. Respondents (a self-selected 4% of the total invited number) were likely to be more interested in the pathogenesis of NAFLD, and their clinical behaviors may not be representative. As the authors concede, it is essential now to investigate both awareness and the degree of understanding among community physicians, for it is there that rational screening with noninvasive tests and holistic approaches to lifestyle and risk factors must occur if economically viable models of care are to be sustained.5
Learning from deep learning and pathomics
Authors: Agnes B. Fogo
Journal: Kidney International (2023)

The suffix -omics has been applied to a variety of approaches with the overarching aim to identify, describe, and quantify processes that contribute to the form and function of cells and tissues. Historically, histopathologic approaches have relied on assessment of lesions to describe a pattern of injury and when possible, give a specific etiologic diagnosis. Broad pathologic entities have been split into smaller groups to provide more individualized diagnostic, prognostic, and etiologic information as a step towards precision medicine. More recently, pathomics has emerged as a complement to traditional histopathology, applying deep learning algorithms to digital histopathology images for detailed quantitative mining of visible or subvisual features that correlate with specific diagnoses, disease trajectories, or shared injury patterns. In a recent publication in Nature Communications, Hölscher and colleagues describe this exciting new approach of pathomics, with the potential to provide insights into kidney disease diagnosis, prognosis, and mechanisms ( 1 Hölscher D.L. Bouteldja N. Joodaki M. et al. Next-Generation Morphometry for pathomics-data mining in histopathology. Nat Commun. 2023; 14: 470 Crossref PubMed Scopus (1) Google Scholar ).
Prognostication in Stargardt Disease Using Fundus Autofluorescence: Improving Patient Care
Authors: Malena Daich Varela, Yannik Laich, Shaima Awadh Hashem, Omar A. Mahroo, Andrew R. Webster, Michel Michaelides
Journal: Ophthalmology (2023)

PurposeTo explore fundus autofluorescence (FAF) imaging as an alternative to electroretinogram (ERG), as a non-invasive, quick, and readily interpretable method to predict disease progression in Stargardt disease (STGD).DesignRetrospective case series of patients who attended Moorfields Eye Hospital (London, UK).SubjectsPatients with STGD who met the following criteria were included: (i) biallelic disease-causing variants in ABCA4, (ii) ERG testing performed inhouse with an unequivocal ERG group classification, and (iii) ultra-widefield (UWF) FAF imaging performed up to 2 years before or after the ERG.MethodsPatients were divided into three ERG groups based on retinal function and three FAF groups according to the extent of the hypoautofluorescence and their retinal background appearance. FAF imaging of 30 and 55° were also subsequently reviewed.Main outcome measuresERG/FAF concordance and its association with baseline visual acuity and genetics.Results234 patients were included in the cohort. 170 patients (73%) had the same ERG and FAF group, 33 (14%) had a milder FAF than ERG group, and 31 (13%) had a more severe FAF than ERG group. Children under the age of 10 (n=23) had the lowest ERG/FAF concordance, 57% (9 out of the 10 with discordant ERG/FAF had milder FAF than ERG), and adults with adult onset had the highest (80%). Missense genotypes were more commonly seen in the mildest phenotypes. In 97% and 98% of the cases, respectively, 30° and 55° FAF imaging matched with the group defined by UWF FAF.ConclusionsWe demonstrate that FAF imaging is an effective modality to determine the extent of retinal involvement and thereby inform prognostication, by comparing FAF to the current gold standard of ERG testing to determine retinal involvement and thereby prognosis. In 80% of patients in our large molecularly proven cohort we were able to predict if the disease was confined to the macula or also affected the peripheral retina. Children assessed at a young age, with at least one null variant, early disease onset, and/or poor initial VA may have wider retinal involvement than predicted by FAF alone and/or progress to a more severe FAF phenotype over time.
Non-invasive chronic kidney disease risk stratification tool derived from retina-based deep learning and clinical factors
Authors: Young Su Joo, Tyler Hyungtaek Rim, Hee Byung Koh, Joseph Yi, Hyeonmin Kim, Geunyoung Lee, Young Ah Kim, Shin-Wook Kang, Sung Soo Kim, Jung Tak Park
Journal: npj Digital Medicine (2023)

Despite the importance of preventing chronic kidney disease (CKD), predicting high-risk patients who require active intervention is challenging, especially in people with preserved kidney function. In this study, a predictive risk score for CKD (Reti-CKD score) was derived from a deep learning algorithm using retinal photographs. The performance of the Reti-CKD score was verified using two longitudinal cohorts of the UK Biobank and Korean Diabetic Cohort. Validation was done in people with preserved kidney function, excluding individuals with eGFR <90 mL/min/1.73 m2 or proteinuria at baseline. In the UK Biobank, 720/30,477 (2.4%) participants had CKD events during the 10.8-year follow-up period. In the Korean Diabetic Cohort, 206/5014 (4.1%) had CKD events during the 6.1-year follow-up period. When the validation cohorts were divided into quartiles of Reti-CKD score, the hazard ratios for CKD development were 3.68 (95% Confidence Interval [CI], 2.88-4.41) in the UK Biobank and 9.36 (5.26-16.67) in the Korean Diabetic Cohort in the highest quartile compared to the lowest. The Reti-CKD score, compared to eGFR based methods, showed a superior concordance index for predicting CKD incidence, with a delta of 0.020 (95% CI, 0.011-0.029) in the UK Biobank and 0.024 (95% CI, 0.002-0.046) in the Korean Diabetic Cohort. In people with preserved kidney function, the Reti-CKD score effectively stratifies future CKD risk with greater performance than conventional eGFR-based methods.
Mucosa‐Mimetic Materials for the Study of Intestinal Homeostasis and Disease
Authors: Rebecca Donahue, Jugal Kishore Sahoo, Sara Rudolph, Ying Chen, David L. Kaplan
Journal: Advanced Healthcare Materials (2023)

Abstract Mucus is a viscoelastic hydrogel that lines and protects the epithelial surfaces of the body that houses commensal microbiota and functions in host defense against pathogen invasion. As a first‐line physical and biochemical barrier, intestinal mucus is involved in immune surveillance and spatial organization of the microbiome, while dysfunction of the gut mucus barrier is implicated in several diseases. Mucus can be collected from a variety of mammalian sources for study, however, established methods are challenging in terms of scale and efficiency, as well as with regard to rheological similarity to native human mucus. Therefore, there is a need for mucus‐mimetic hydrogels that more accurately reflect the physical and chemical profile of the in vivo human epithelial environment to enable the investigation of the role of mucus in human disease and interactions with the intestinal microbiome. This review will evaluate the material properties of synthetic mucus mimics to date designed to address the above need, with a focus toward an improved understanding of the biochemical and immunological functions of these biopolymers related to utility for research and therapeutic applications.
A meta-analysis of GFR slope as a surrogate endpoint for kidney failure
Authors: Lesley A. Inker, Willem Collier, Tom Greene, Shiyuan Miao, Juhi Chaudhari, Gerald B. Appel, Sunil V. Badve, Fernando Caravaca-Fontán, Lucia Del Vecchio, Jürgen Floege, Marian Goicoechea, Benjamin Haaland, William G. Herrington, Enyu Imai, Tazeen H. Jafar, Julia B. Lewis, Philip K. T. Li, Bart D. Maes, Brendon L. Neuen, Ronald D. Perrone, Giuseppe Remuzzi, Francesco P. Schena, Christoph Wanner, Jack F. M. Wetzels, Mark Woodward, Hiddo J. L. Heerspink, Raymond O. Estacio, Rebecca Hanratty, John Chalmers, Pietro Canetta, Brendan Barrett, Bruce Neal, Vlado Perkovic, Kenneth W. Mahaffey, David Johnson, Meg Jardine, Maximilian von Eynatten, Eduardo Verde, Ursula Verdalles, David Arroyo, Arlene Chapman, Vicente Torres, Alan Yu, Godela Brosnahan, Thierry Hannedouche, Kai-Ming Chow, Cheuk-Chun Szeto, Chi-Bon Leung, Di Xie, Fan Fan Hou, Jamie Dwyer, Marc A. Pohl, Itamar Raz, Lawrence G. Hunsicker, An Vanacker, Thomas Malfait, Giuseppe Maschio, Francesco Locatelli, Peter J. Blankestijn, Arjan van Zuilen, Fumiaki Kobayashi, Hirofumi Makino, Juliana C. N. Chan, Simeone Andrulli, Claudio Pozzi, Donatella Casartelli, Manuel Praga, Hernando Trujillo, Teresa Cavero, Angel Sevillano, Piero Ruggenenti, Annalisa Perna, Fabiola Carrara, William F. Keane, Carlo Manno, Richard Haynes, William G. Herrington, Colin Baigent, Martin Landray, Thomas Rauen, Claudia Seikrit, Stefanie Wied, Robert D. Toto, Paul E. de Jong, Mauro Saddelli
Journal: Nature Medicine (2023)
Gut microbiota controlling radiation-induced enteritis and intestinal regeneration
Authors: Ilias Moraitis, Jordi Guiu, Josep Rubert
Journal: Trends in Endocrinology and Metabolism (2023)

Cancer remains the second leading cause of mortality, with nearly 10 million deaths worldwide in 2020. In many cases, radiotherapy is used for its anticancer effects. However, radiation causes healthy tissue toxicity as a side effect. In intra-abdominal and pelvic malignancies, the healthy bowel is inevitably included in the radiation field, causing radiation-induced enteritis and dramatically affecting the gut microbiome. This condition is associated with significant morbidity and mortality that impairs cancer patients' and survivors' quality of life. This Review provides a critical overview of the main drivers in modulating the gut microenvironment in homeostasis, disease, and injury, focusing on gut microbial metabolites and microorganisms that influence epithelial regeneration upon radiation injury.
A cell-free tissue-engineered tracheal substitute with sequential cytokine release maintained airway opening in a rabbit tracheal full circumferential defect model
Authors: Yujian Liu, Kaifu Zheng, Zijie Meng, Lei Wang, Xi Liu, Baolin Guo, Jiankang He, Xiyang Tang, Mingyao Liu, Nan Ma, Xiaofei Li, Jinbo Zhao
Journal: Biomaterials (2023)

In this study, a cell-free tissue-engineered tracheal substitute was developed, which is based on a 3D-printed polycaprolactone scaffold coated with a gelatin-methacryloyl (GelMA) hydrogel, with transforming growth factor-β1 (TGF-β) and stromal cell-derived factor-1α (SDF-1) sequentially embedded, to facilitate cell recruitment and differentiation toward chondrocyte-phenotype. TGF-β was loaded onto polydopamine particles, and then encapsulated into the GelMA together with SDF-1, and called G/S/P@T, which was used to coat 3D-printed PCL scaffold to form the tracheal substitute. A rapid release of SDF-1 was observed during the first week, followed by a slow and sustained release of TGF-β for approximately four weeks. The tracheal substitute significantly promoted the recruitment of mesenchymal stromal cells (MSCs) or human bronchial epithelial cells in vitro, and enhanced the ability of MSCs to differentiate towards chondrocyte phenotype. Implantation of the tissue-engineered tracheal substitute with a rabbit tracheal anterior defect model improved regeneration of airway epithelium, recruitment of endogenous MSCs and expression of markers of chondrocytes at the tracheal defect site. Moreover, the tracheal substitute maintained airway opening for 4 weeks in a tracheal full circumferential defect model with airway epithelium coverage at the defect sites without granulation tissue accumulation in the tracheal lumen or underneath. The promising results suggest that this simple, cell-free tissue-engineered tracheal substitute can be used directly after tracheal defect removal and should be further developed towards clinical application.
Social determinants of health and US cancer screening interventions: A systematic review
Authors: Ariella R. Korn, Callie Walsh‐Bailey, Margarita Correa‐Mendez, Peter DelNero, Meagan Pilar, Brittney Sandler, Ross C. Brownson, Karen M. Emmons, April Y. Oh
Journal: CA A Cancer Journal for Clinicians (2023)

Abstract There remains a need to synthesize linkages between social determinants of health (SDOH) and cancer screening to reduce persistent inequities contributing to the US cancer burden. The authors conducted a systematic review of US‐based breast, cervical, colorectal, and lung cancer screening intervention studies to summarize how SDOH have been considered in interventions and relationships between SDOH and screening. Five databases were searched for peer‐reviewed research articles published in English between 2010 and 2021. The Covidence software platform was used to screen articles and extract data using a standardized template. Data items included study and intervention characteristics, SDOH intervention components and measures, and screening outcomes. The findings were summarized using descriptive statistics and narratives. The review included 144 studies among diverse population groups. SDOH interventions increased screening rates overall by a median of 8.4 percentage points (interquartile interval, 1.8–18.8 percentage points). The objective of most interventions was to increase community demand (90.3%) and access (84.0%) to screening. SDOH interventions related to health care access and quality were most prevalent (227 unique intervention components). Other SDOH, including educational, social/community, environmental, and economic factors, were less common (90, 52, 21, and zero intervention components, respectively). Studies that included analyses of health policy, access to care, and lower costs yielded the largest proportions of favorable associations with screening outcomes. SDOH were predominantly measured at the individual level. This review describes how SDOH have been considered in the design and evaluation of cancer screening interventions and effect sizes for SDOH interventions. Findings may guide future intervention and implementation research aiming to reduce US screening inequities.
Pharmacotherapy for obstructive sleep apnea - A systematic review and meta-analysis of randomized controlled trials
Authors: Yi-Chieh Lee, Chun-Ting Lu, Li-Pang Chuang, Li-Ang Lee, Tuan-Jen Fang, Wen-Nuan Cheng, Hsueh-Yu Li
Journal: Sleep Medicine Reviews (2023)

Continuous positive airway pressure is the first-line and gold-standard treatment for obstructive sleep apnea (OSA). Pharmacotherapy is not commonly used in treating OSA until recently. Combined noradrenergic and antimuscarinic agents have been clinically applied for OSA patients with variable results. This meta-analysis study aimed to investigate the efficacy of the combined regimen on OSA. A systematic literature search was performed up to November 2022 for the effects of the combined regimen on OSA. Eight randomized controlled trials were identified and systematically reviewed for meta-analysis. There were significant mean differences between OSA patients taking a combined regimen and placebo in apnea-hypopnea index (AHI) [mean difference (MD) -9.03 events/h, 95%CI (-16.22, -1.83 events/h; P = 0.01] and lowest oxygen saturation [MD 5.61%, 95% CI % (3.43, 7.80); P < 0.01]. Meta-regression showed that a higher proportion of male participants was associated with a greater reduction of AHI (p = 0.04). This study showed a positive but modest effect of pharmacotherapy in the reduction of OSA severity. The combination drugs are most applicable to male OSA patients based on their efficacy and pharmacological susceptibility. Pharmacotherapy may be applied as an alternative, adjunctive or synergistic treatment under careful consideration of its side effects.
What Are the Short-term Benefits and Potential Harms of Therapeutic Modalities for the Management of Overactive Bladder Syndrome in Women? A Review of Evidence Under the Auspices of the European Association of Urology, Female Non-neurogenic Lower Urinary Tract Symptoms Guidelines Panel
Authors: Fawzy Farag, Vasileios I. Sakalis, Serenella Monagas Arteaga, Néha Sihra, Markos Karavitakis, Salvador Arlandis, Kari Bø, Hanny Cobussen-Boekhorst, Elisabetta Costantini, Monica de Heide, Jan Groen, Benoit Peyronnet, Veronique Phé, Mary-Lynne van Poelgeest-Pomfret, Tine W.L. van den Bos, Huub van der Vaart, Christopher K. Harding, Marie Carmela Lapitan, Muhammad Imran Omar, Arjun K. Nambiar
Journal: European Urology (2023)
Gelatin nanofiber-reinforced decellularized amniotic membrane promotes axon regeneration and functional recovery in the surgical treatment of peripheral nerve injury
Authors: Long Chen, Xiongbo Song, Zhicheng Yao, Conglai Zhou, Junjun Yang, Qiming Yang, Junrong Chen, Jiarui Wu, Zeyu Sun, Liling Gu, Yi Ma, Shin-Jae Lee, Chi Zhang, Hai-Quan Mao, Li Sun
Journal: Biomaterials (2023)
External validation of multiple prognosis scores to guide usage of echocardiography in patients with Staphylococcus aureus bacteremia using a prospective cohort
Authors: Clémentin Vignau, Marion Le Maréchal, Carole Saunier, Yvan Caspar, Caroline Landelle, Marie Froidure, Myriam Blanc, Patricia Pavese
Journal: Journal of Infection (2023)
Balanced crystalloid solution versus saline in deceased donor kidney transplantation (BEST-Fluids): a pragmatic, double-blind, randomised, controlled trial
Authors: Michael G Collins, Magid A Fahim, Elaine M Pascoe, Carmel M Hawley, David W Johnson, Julie Varghese, Laura E Hickey, Philip A Clayton, Kathryn B Dansie, Rachael C McConnochie, Liza A Vergara, Charani Kiriwandeniya, Donna Reidlinger, Peter F Mount, Laurence Weinberg, Colin J McArthur, P Toby Coates, Zoltan H Endre, David Goodman, Kirsten Howard, Martin Howell, Jagadish S Jamboti, John Kanellis, Jerome M Laurence, Wai H Lim, Steven J McTaggart, Philip J O'Connell, Helen L Pilmore, Germaine Wong, Steven J Chadban, Steven J Chadban, Tracey Ying, David Gracey, Leyla Aouad, Kate Wyburn, Beatriz Habijanec, Hee-eun (Ellen) Yeo, Lin Lin, Brenda Rosales, Julia Hudaly, Vera Rodrigues, Germaine Wong, Philip O'Connell, Penelope Murie, Zoltan Endre, Zuzana Gray, Rebecca Spicer, Anne Durkan, Magid A Fahim, Dev Jegatheesan, Diana Leary, Yujing (Sarah) Guo, Amanda Coburn, Rachael Irvine, Steven McTaggart, Aimee Crawford, P Toby Coates, Bronwyn Hockley, Karen Fischer, Laurence Weinberg, Peter Mount, Sarah Baulch, Gayle Claxton, Saskia Harris, Sofia Sidiropoulos, Marieke Veenendal, John Kanellis, Rita Barbis, David Goodman, Anjalee Brahmbhatt, Amelia Le Page, Jagadish Jamboti, Anna Chiam, Anne Warger, Wai H Lim, Michael Collins, Helen Pilmore, Ian Dittmer, Paul Manley, Jafar Ahmed, Rachael McConnochie, Lynette Newby, Yan Chen, Catherine Simmonds, John Irvine, Jenny Usher, Carolyn Clark, Claire Beckett, Chanel Prestidge, Robin Erickson, Miriam Rea, Claire Scherring
Journal: The Lancet (2023)
Glucagon-like Peptide-1 Receptor Agonist Use in Patients With Liver Cirrhosis and Type 2 Diabetes
Authors: Fu-Shun Yen, Ming-Chih Hou, James Cheng-Chung Wei, Ying-Hsiu Shih, Chung Y. Hsu, Chih-Cheng Hsu, Chii-Min Hwu
Journal: Clinical Gastroenterology and Hepatology (2023)
Antimicrobial susceptibility assays for Neisseria gonorrhoeae: a proof-of-principle population-based retrospective analysis
Authors: Sara F E Bell, Robert S Ware, David A Lewis, Monica M Lahra, David M Whiley
Journal: The Lancet Microbe (2023)

Neisseria gonorrhoeae treatment guided by molecular antimicrobial susceptibility assays could improve treatment options and antimicrobial stewardship; however, few commercial assays are available. We aimed to investigate antimicrobial susceptibility of N gonorrhoeae isolates in New South Wales, Australia, and estimate the potential usefulness of hypothetical combinations of rapid molecular antimicrobial susceptibility assays.
Application of stem cells in regeneration medicine
Authors: Ye Jin, Shuangyang Li, Qixuan Yu, Tianli Chen, Da Liu
Journal: MedComm (2023)

Abstract Regeneration is a complex process affected by many elements independent or combined, including inflammation, proliferation, and tissue remodeling. Stem cells is a class of primitive cells with the potentiality of differentiation, regenerate with self‐replication, multidirectional differentiation, and immunomodulatory functions. Stem cells and their cytokines not only inextricably linked to the regeneration of ectodermal and skin tissues, but also can be used for the treatment of a variety of chronic wounds. Stem cells can produce exosomes in a paracrine manner. Stem cell exosomes play an important role in tissue regeneration, repair, and accelerated wound healing, the biological properties of which are similar with stem cells, while stem cell exosomes are safer and more effective. Skin and bone tissues are critical organs in the body, which are essential for sustaining life activities. The weak repairing ability leads a pronounced impact on the quality of life of patients, which could be alleviated by stem cell exosomes treatment. However, there are obstacles that stem cells and stem cells exosomes trough skin for improved bioavailability. This paper summarizes the applications and mechanisms of stem cells and stem cells exosomes for skin and bone healing. We also propose new ways of utilizing stem cells and their exosomes through different nanoformulations, liposomes and nanoliposomes, polymer micelles, microspheres, hydrogels, and scaffold microneedles, to improve their use in tissue healing and regeneration.